Efficient assembly of nanopore reads via highly accurate and intact error correction
Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences d...
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| Published in | Nature communications Vol. 12; no. 1; pp. 60 - 10 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
04.01.2021
Nature Publishing Group Nature Portfolio |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2041-1723 2041-1723 |
| DOI | 10.1038/s41467-020-20236-7 |
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| Abstract | Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.
Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopore reads. |
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| AbstractList | Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection. Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection. Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection. Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopore reads. Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopore reads. Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopore reads. |
| ArticleNumber | 60 |
| Author | Xie, Shang-Qian Huang, Zhi-Jian Chen, Ying Wang, Jian-Xin Liu, Yi-Zhi Nie, Fan Xing, Jian-Feng He, Li-Juan Bray, Thomas Dai, Qi Wang, De-Peng Wang, Yao-Xin Xiao, Chuan-Le Luo, Feng Zheng, Ying-Feng |
| Author_xml | – sequence: 1 givenname: Ying surname: Chen fullname: Chen, Ying organization: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University – sequence: 2 givenname: Fan surname: Nie fullname: Nie, Fan organization: School of Information Science and Engineering, Central South University – sequence: 3 givenname: Shang-Qian surname: Xie fullname: Xie, Shang-Qian organization: Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University – sequence: 4 givenname: Ying-Feng surname: Zheng fullname: Zheng, Ying-Feng organization: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University – sequence: 5 givenname: Qi surname: Dai fullname: Dai, Qi organization: College of Life Sciences and Medicine, Zhejiang Sci-Tech University – sequence: 6 givenname: Thomas surname: Bray fullname: Bray, Thomas organization: Oxford Nanopore Technologies – sequence: 7 givenname: Yao-Xin surname: Wang fullname: Wang, Yao-Xin organization: College of Life Sciences and Medicine, Zhejiang Sci-Tech University – sequence: 8 givenname: Jian-Feng surname: Xing fullname: Xing, Jian-Feng organization: Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, Hainan University, Hainan Key Laboratory for Biology of Tropical Ornamental Plant Germplasm, College of Forestry, Hainan University – sequence: 9 givenname: Zhi-Jian orcidid: 0000-0003-1601-3802 surname: Huang fullname: Huang, Zhi-Jian organization: School of Marine Sciences, Sun Yat-sen University, State Key Laboratory of Biocontrol, Sun Yat-sen University, Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University – sequence: 10 givenname: De-Peng surname: Wang fullname: Wang, De-Peng organization: Nextomics Biosciences Co., Ltd – sequence: 11 givenname: Li-Juan surname: He fullname: He, Li-Juan organization: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University – sequence: 12 givenname: Feng orcidid: 0000-0002-4813-2403 surname: Luo fullname: Luo, Feng email: luofeng@clemson.edu organization: School of Computing, Clemson University – sequence: 13 givenname: Jian-Xin orcidid: 0000-0003-1516-0480 surname: Wang fullname: Wang, Jian-Xin email: jxwang@mail.csu.edu.cn organization: School of Information Science and Engineering, Central South University, Hunan Provincial Key Lab on Bioinformatics, Central South University – sequence: 14 givenname: Yi-Zhi surname: Liu fullname: Liu, Yi-Zhi email: liuyizh@mail.sysu.edu.cn organization: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Research Units of Ocular Development and Regeneration, Chinese Academy of Medical Sciences – sequence: 15 givenname: Chuan-Le orcidid: 0000-0002-4680-0682 surname: Xiao fullname: Xiao, Chuan-Le email: xiaochuanle@126.com organization: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33397900$$D View this record in MEDLINE/PubMed |
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| Copyright | The Author(s) 2021 The Author(s) 2021. This work is published under https://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. |
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| DOI | 10.1038/s41467-020-20236-7 |
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| Snippet | Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate... Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and... |
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| SubjectTerms | 45/23 631/114/2397 631/208/212/2302 631/208/514/1948 Assembling Assembly Cell Line Chromosomes, Human - genetics Error correction Error correction & detection Error reduction Genome, Human Genomes Humanities and Social Sciences Humans multidisciplinary Nanopores Porosity Retinoblastoma - genetics Science Science (multidisciplinary) Sequence Analysis, DNA Software |
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| Title | Efficient assembly of nanopore reads via highly accurate and intact error correction |
| URI | https://link.springer.com/article/10.1038/s41467-020-20236-7 https://www.ncbi.nlm.nih.gov/pubmed/33397900 https://www.proquest.com/docview/2474981669 https://www.proquest.com/docview/2475398025 https://pubmed.ncbi.nlm.nih.gov/PMC7782737 https://doaj.org/article/38b07015c4a4482d87dff528f09c3e09 |
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